Variant report

Variant	rs12990898
Chromosome Location	chr2:55382026-55382027
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55366215..55370139-chr2:55381125..55383848,4	K562	blood:
2	chr2:55276755..55278811-chr2:55380705..55382664,2	K562	blood:
3	chr2:55381461..55384180-chr2:55385114..55387794,2	MCF-7	breast:
4	chr2:55366215..55370313-chr2:55376970..55382641,6	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11125555	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11125556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133181	0.83[CHB][hapmap]
rs12470651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621144	0.83[CHB][hapmap]
rs12623137	0.80[JPT][hapmap]
rs2576711	0.82[JPT][hapmap]
rs2589096	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs3935223	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs4672024	0.83[CHB][hapmap]
rs4672025	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672026	0.80[ASN][1000 genomes]
rs6545475	0.82[CHB][hapmap]
rs66483070	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6715130	0.84[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7595134	0.83[CHB][hapmap]
rs7608118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12990898	CLHC1	cis	Nerve Tibial	GTEx
rs12990898	CLHC1	cis	Artery Tibial	GTEx
rs12990898	VRK2	cis	parietal	SCAN
rs12990898	PRDXDD1P	cis	cerebellum	SCAN
rs12990898	PSME4	cis	parietal	SCAN
rs12990898	FLJ31438	cis	multi-tissue	Pritchard
rs12990898	CLHC1	cis	Adipose Subcutaneous	GTEx
rs12990898	CLHC1	cis	lung	GTEx
rs12990898	CLHC1	cis	Thyroid	GTEx
rs12990898	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs12990898	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55371600-55382400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:55376000-55383800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:55376800-55382400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:55378000-55386800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:55378000-55386800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:55378200-55382400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:55378200-55383600	Enhancers	Brain Substantia Nigra	brain
8	chr2:55378200-55386200	Enhancers	Brain Hippocampus Middle	brain
9	chr2:55378200-55388000	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:55378200-55388800	Enhancers	Adipose Nuclei	Adipose
11	chr2:55378400-55383800	Enhancers	NHLF	lung
12	chr2:55378600-55383200	Enhancers	Colon Smooth Muscle	Colon
13	chr2:55378600-55383600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:55378600-55385600	Enhancers	Rectal Smooth Muscle	rectum
15	chr2:55378600-55386800	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr2:55378600-55386800	Enhancers	Fetal Stomach	stomach
17	chr2:55378800-55382600	Enhancers	Placenta	Placenta
18	chr2:55378800-55383200	Enhancers	Fetal Brain Male	brain
19	chr2:55378800-55383600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:55378800-55385600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:55378800-55386800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr2:55379000-55384200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr2:55379200-55383000	Enhancers	Fetal Brain Female	brain
24	chr2:55379200-55383600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:55379200-55385200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:55379400-55385200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:55379400-55386600	Enhancers	Fetal Intestine Large	intestine
28	chr2:55379400-55387000	Enhancers	Fetal Intestine Small	intestine
29	chr2:55379600-55382200	Enhancers	K562	blood
30	chr2:55379600-55385000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:55379600-55386800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr2:55380000-55384400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:55380200-55382600	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr2:55380200-55386000	Enhancers	Hela-S3	cervix
35	chr2:55380400-55384400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:55380600-55383800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:55380600-55384000	Enhancers	Fetal Heart	heart
38	chr2:55380600-55384000	Enhancers	HMEC	breast
39	chr2:55380800-55382200	Enhancers	Colonic Mucosa	Colon
40	chr2:55380800-55382400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr2:55380800-55382400	Enhancers	HSMMtube	muscle
42	chr2:55380800-55382800	Enhancers	A549	lung
43	chr2:55380800-55383000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:55380800-55383400	Enhancers	NHDF-Ad	bronchial
45	chr2:55380800-55383600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:55380800-55385400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:55381000-55382400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:55381000-55382400	Enhancers	Right Atrium	heart
49	chr2:55381000-55382400	Enhancers	Osteobl	bone
50	chr2:55381000-55382600	Enhancers	Esophagus	oesophagus

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